Comparative transcriptomic analyses revealed divergences of two agriculturally important aphid species (original) (raw)
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Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont.
We propose sequencing of the 300Mb nuclear genome of the pea aphid, Acyrthosiphon pisum. Aphids display a diversity of biological problems that are not easily studied in other genetic model systems. First, because they are the premier model for the study of bacterial endosymbiosis and because they vector many well-studied plant viruses, aphids are an excellent model for studying animal interactions with microbes. Second, because their normal life cycle displays extreme developmental plasticity as well as both clonal and sexual reproduction, aphids provide the opportunity to understand the basis of phenotypic plasticity as well as the genomic consequences of sexual versus asexual reproduction. Their alternative reproductive modes can also be exploited in genetic experiments, because clones can be maintained indefinitely in the laboratory with sexual generations induced at will 1,2. Third, aphids provide some of the best studied instances of adaptation, in the form of both insecticide resistance, which has evolved through several molecular mechanisms, and host plant adaptation, which has repeatedly generated novel aphid lineages specialized to particular crop plant cultivars and which is presumably the basis for the radiation of aphids onto many specialized host plants during their long evolutionary history. Finally, an aphid genome will provide important phylogenetic information, serving as an outgroup to the many genomes being sequenced in holometabolous insects (flies, beetles, bees, moths) and providing a valuable resource for annotation of the genomes of other hemimetabolous insects, most of which have much larger genomes than the aphid. Aphid biology is relevant to human health in several ways. First, aphids cause crop damage on the order of hundreds of millions of dollars in lost production each year 3,4. Second, pest aphid populations are controlled primarily by pesticides. These pesticides may persist on harvested crops and in the environment, to the detriment of human health and environmental quality. Third, bacterial symbiosis in aphids may serve as a general model for understanding processes of bacterial infection 5-7. Fourth, aphids transmit some viruses in ways that resemble insect-borne human viruses and thus provide models for studying insect-vector viral disease 8,9. Finally, because aphids display dramatic phenotypic plasticity 10,11 , they provide a model system for how environmental and genetic factors interact in determining the phenotype. There is growing awareness that phenotypic plasticity, for example differential response to drugs, is an important component of human welfare 12. As a group, aphids are among the most intensively studied insects and are the focus of a large community of researchers. Several labs have developed genomic tools for studying aphids, including genetic maps, BAC libraries, EST sequences and microarrays.
Molecular Ecology, 2012
A major goal in evolutionary biology is to uncover the genetic basis of adaptation. Divergent selection exerted on ecological traits may result in adaptive population differentiation and reproductive isolation and affect differentially the level of genetic divergence along the genome. Genome-wide scan of large sets of individuals from multiple populations is a powerful approach to identify loci or genomic regions under ecologically divergent selection. Here, we focused on the pea aphid, a species complex of divergent host races, to explore the organization of the genomic divergence associated with host plant adaptation and ecological speciation. We analysed 390 microsatellite markers located at variable distances from predicted genes in replicate samples of sympatric populations of the pea aphid collected on alfalfa, red clover and pea, which correspond to three common host-adapted races reported in this species complex. Using a method that accounts for the hierarchical structure of our data set, we found a set of 11 outlier loci that show higher genetic differentiation between host races than expected under the null hypothesis of neutral evolution. Two of the outliers are close to olfactory receptor genes and three other nearby genes encoding salivary proteins. The remaining outliers are located in regions with genes of unknown functions, or which functions are unlikely to be involved in interactions with the host plant. This study reveals genetic signatures of divergent selection across the genome and provides an inventory of candidate genes responsible for plant specialization in the pea aphid, thereby setting the stage for future functional studies.
Genome sequence of the corn leaf aphid (Rhopalosiphum maidisFitch)
GigaScience, 2019
Background: The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the world's most important grain crops. In addition to causing direct damage by removing photoassimilates, R. maidis transmits several destructive maize viruses, including maize yellow dwarf virus, barley yellow dwarf virus, sugarcane mosaic virus, and cucumber mosaic virus. Findings: The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of Pacific Biosciences (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 megabases (Mb) and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into 4 scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both Pacific Biosciences and Illumina. An analysis of likely horizontally transferred genes identified 2 from bacteria, 7 from fungi, 2 from protozoa, and 9 from algae. Repeat elements, transposons, and genes encoding likely detoxification enzymes (cytochrome P450s, glutathione S-transferases, carboxylesterases, uridine diphosphate-glucosyltransferases, and ABC transporters) were identified in the genome sequence. Other than Buchnera aphidicola (642,929 base pairs, 602 genes), no endosymbiont bacteria were found in R. maidis. Conclusions: A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.
Genome Biology and Evolution
In theory, the loss of sexual reproduction is expected to result in the accumulation of deleterious mutations. In aphids, two main types of life cycle, cyclic and obligate parthenogenesis, represent respectively ''sexual'' and ''asexual'' reproductive modes. We used the complete pea aphid genome and previously published expressed sequence tags (ESTs) from two other aphid species. In addition, we obtained 100,000 new ESTs from five more species. The final set comprised four sexual and four asexual aphid species and served to test the influence of the reproductive mode on the evolutionary rates of genes. We reconstructed coding sequences from ESTs and annotated these genes, discovering a novel peptide gene family that appears to be among the most highly expressed transcripts from several aphid species. From 203 genes found to be 1:1 orthologs among the eight species considered, we established a species tree that partly conflicted with taxonomy (for Myzus ascalonicus). We then used this topology to evaluate the dynamics of evolutionary rates and mutation accumulation in the four sexual and four asexual taxa. No significant increase of the nonsynonymous to synonymous ratio or of nonsynonymous mutation numbers was found in any of the four branches for asexual taxa. We however found a significant increase of the synonymous rate in the branch leading to the asexual species Rhopalosiphum maidis, which could be due to a change in the mutation rate or to an increased number of generations implied by its change of life cycle.
Insect Molecular Biology, 2010
Phylogenetic analyses serve many purposes, including the establishment of orthology relationships, the prediction of protein function and the detection of important evolutionary events. Within the context of the sequencing of the genome of the pea aphid, Acyrthosiphon pisum, we undertook a phylogenetic analysis for every protein of this species. The resulting phylome includes the evolutionary relationships of all predicted aphid proteins and their homologues among 13 other fully-sequenced arthropods and three out-group species. Subsequent analyses have revealed multiple gene expansions that are specific to aphids and have served to transfer functional annotations to 4058 pea aphid genes that display one-to-one orthology relationships with Drosophila melanogaster annotated genes. All phylogenies and alignments are accessible through the PhylomeDB database. Here we provide a description of this dataset and provide some examples on how can it be exploited.
Genome sequence of the pea aphid Acyrthosiphon pisum
2010
Abstract Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects.